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Protocols

UniPROBE specifications

Information


Unique identifier OMICS_00546
Name UniPROBE
Alternative name Universal PBM Resource for Oligonucleotide Binding Evaluation
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans
    • Plasmodium falciparum
  • Plants and Fungi
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Maintainer


  • person_outline Martha Bulyk

Publications for Universal PBM Resource for Oligonucleotide Binding Evaluation

UniPROBE citations

 (79)
library_books

Degenerate Pax2 and Senseless binding motifs improve detection of low affinity sites required for enhancer specificity

2018
PLoS Genet
PMCID: 5902045
PMID: 29617378
DOI: 10.1371/journal.pgen.1007289

[…] ssing read quality with FASTQC [] (–); mapping to the mm10 genome using Bowtie 2 []; and calling and scoring peaks using MACS2 [].PBM data were downloaded from CIS-BP (D. rerio Pax2b, M1499_1.02) and UniPROBE (H. sapiens Gfi1b, UP00592) [, ]. AUROC analysis was done on PBM probes binned by fluorescence (top 0.25%, top 0.5%-0.25%, top 1%-0.5%, top 2.5%-1%, top 5%-1%, top 10%-5%). For each bin, cont […]

library_books

A unified approach for quantifying and interpreting DNA shape readout by transcription factors

2018
Mol Syst Biol
PMCID: 5822049
PMID: 29472273
DOI: 10.15252/msb.20177902

[…] maximizing the number of bases matching the top 10mer, then constructed a frequency matrix from these alignments, and, finally, used this frequency matrix to align the retained SELEX probes. For the UniPROBE and CIS‐BP PBM datasets, we selected the 100 probes with the strongest binding signal and aligned these to the curated scoring matrix. We finally used the pentamer tables to compute the mean […]

library_books

Identification of Single Nucleotide Non coding Driver Mutations in Cancer

2018
Front Genet
PMCID: 5801294
PMID: 29456552
DOI: 10.3389/fgene.2018.00016

[…] ext generation sequencing (ChIP-seq) (; ; ). Currently, DNA binding specificities have been determined for nearly half of human TFs, which are available in different repositories such CIS-BP, Jaspar, Uniprobe, and Transfac (; ; ; ) (Table ). Differences in TF binding between SNV alleles can be predicted using position weight matrices (PWMs), probabilistic representations of DNA binding specificiti […]

library_books

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

2017
Sci Rep
PMCID: 5686184
PMID: 29138457
DOI: 10.1038/s41598-017-15822-7

[…] enhancers.We determined the enrichment of 466 TFs in eRNA regions and weakly-transcribed enhancers using FIMO with the default parameters. The TF motifs were collected from the Transfac, Jaspar, and UniProbe databases. A motif was retained only when it was significantly overrepresented (P ≤ 0.01) compared with the background sets. We used the binomial distribution test to calculate the P-values o […]

library_books

Hypomethylated domain enriched DNA motifs prepattern the accessible nucleosome organization in teleosts

2017
PMCID: 5607494
PMID: 28931432
DOI: 10.1186/s13072-017-0152-2

[…] TOMTOM [] was used to search motifs similar to 6-mers. JASPAR Vertebrates and UniPROBE Mouse databases were used as target motifs. […]

library_books

Sox5 regulates beta cell phenotype and is reduced in type 2 diabetes

2017
Nat Commun
PMCID: 5467166
PMID: 28585545
DOI: 10.1038/ncomms15652

[…] tif match analysis was performed using the motif matching tool available in Biopython with a false positive rate of 0.0001 in these regions. Motifs were obtained in Jaspar, Transfact (public) and the Uniprobe databases. The same procedure was repeated 100 times on random genomic regions with the same length as the original regions. We employed a one-tailed Fisher's Exact test to measure if the pro […]

Citations

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UniPROBE institution(s)
Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA; Bioinformatics Graduate Program, Northeastern University, Boston, MA, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, USA; Bioinformatics and Integrative Genomics Graduate Program, Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
UniPROBE funding source(s)
Supported by National Institutes of Health [R01 HG003985] and National Science Foundation Graduate Research Fellowship.

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